This is how The Thunderwing timeline goes in My Little Pony Transformers Prime: The Cutie Re-Mark.

[Twilight, Spike, Optimus, and Starlight arrive in the Everfree Forest]

Starlight Glimmer: The Everfree Forest?

Optimus Prime: Well, that is strange.

Spike: Very strange.

Twilight Sparkle: Why would the map bring us here?

[Suddenly, Timber Wolves appear and attack them]

Twilight Sparkle: Timber Wolves!

Spike: What do we do?

Optimus Prime: [bring out his gun] You run, I'll hold them off.

Starlight Glimmer: Okay.

[Twilight, Spike, and Starlight run while Optimus fights the Timber Wolves]

[Optimus manages to fight them off]

Starlight Glimmer: Whoa. That was fast.

Optimus Prime: I told you.

Spike: Wait. Hold on, guys.

Twilight Sparkle: What is it, Spike?

[They see a castle in the distance]

Twilight Sparkle: Whoa.

Spike: Wow.

Optimus Prime: Since when the Princesses referbish their castle?

Starlight Glimmer: I don't know.

[They head over to it]

[They open the door and find the hallway is abandoned]

Starlight Glimmer: Who would decorate the castle so beautifully and just leave it?

Optimus Prime: I do not know.

Spike: Nor do I.

Twilight Sparkle: Hey, look. There's Rarity.

[They see Rarity doing some dusting]

Starlight Glimmer: We came here through time travel.

Optimus Prime: Pursuing her brother.

Spike: He's trying to alter the past.

Twilight Sparkle: And we're trying to stop him.

Thunderwing: Time travel?

[They look up and see Thunderwing sitting on his throne]

Thunderwing: Now that's something I like to see.

[He flies down]

Thunderwing: Tell me how you came by this magic to travel through time.

[They look at each other and nod]

Twilight Sparkle: Well, you see.

Spike: Somepony used it.

Optimus Prime: And we are trying to get it back.

Starlight Glimmer: Before he transforms the space time continuem.

Thunderwing: Nobody in my kingdom but me should possess a magic powerful enough to change time.

Spike: Your kingdom?

Thunderwing: Who else?

Spike: Princess Luna and Princess Celestia.

[Thunderwing scoffs]

Thunderwing: Banished!

Twilight Sparkle: What?!

Spike: What?!

Optimus Prime: What?!

Starlight Glimmer: What?!

Thunderwing: Now, reveal the source of this time magic to me.

Twilight Sparkle: We can take you to it, but you'll have to get past the Timber Wolves.

Starlight Glimmer: She's right.

Thunderwing: I am the ruler of all of Equestria. Do you think I can't deal with Timber Wolves?

Twilight Sparkle: No. We know you can.

Starlight Glimmer: Just try to be tempted to much.

Thunderwing: And if you were thinking of trying to escape....[he chains up Spike and Optimus] would be very unfortunate for your friends.

[Later, they head for the Cutie Map, Thunderwing blasting a Timber Wolf out of their way as they walk]

Thunderwing: How does it work?

Twilight Sparkle: A pony from our time used this spell to travel back and change the past.

Starlight Glimmer: And that pony is my brother.

Thunderwing: And now you will give this spell to me! With it, I will ensure that the Elements of Harmony are never found and my reign lasts forever!

Twilight Sparkle: No it won't!

Starlight Glimmer: Forget it!

Thunderwing: What?!

Twilight Sparkle: We don't have it.

Starlight Glimmer: If you want it, you'll have to ask the pony who has it.

Thunderwing: Very well.

[Thunderwing attacks Starlight and Twilight frees Optimus and Spike]

[A guard bot shows up and it's about to attack when Optimus pounces on it, knocking off its helmet, revealing the face of Arcee]